16S Amplicon Analysis Report

Generated: 2025-07-27 15:59:41

Sections: alpha_diversity, shap, violin

Table of Contents

Analysis Summary

Top Features

Features associated with nuclear_contamination_status=True

Feature Taxonomic Level Test Effect Size P-value Direction Functions
d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae family ttest 8.7285 5.29e-05 positive
d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales order ttest 7.2508 1.57e-03 positive
d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Comamonadaceae family ttest 7.0821 1.00e-10 positive
d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae family ttest 5.0340 2.38e-07 positive
d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales order ttest 4.6415 1.30e-06 positive
d__Bacteria;p__Dependentiae;c__Babeliae class ttest 4.5236 1.73e-07 positive
d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales order ttest 4.4370 2.84e-07 positive
d__Bacteria;p__Dependentiae phylum ttest 4.1622 1.03e-06 positive
d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Comamonadaceae;g__Comamonas genus ttest 3.8361 1.00e-10 positive
d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pectobacteriaceae;g__Dickeya genus ttest 3.6117 1.00e-10 positive fermentation
d__Bacteria;p__Verrucomicrobiota;c__Chlamydiae;o__Chlamydiales order ttest 3.5409 1.03e-06 positive intracellular_parasites
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;__;__ genus ttest 3.3662 1.00e-10 positive
d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pectobacteriaceae family ttest 3.2440 1.00e-10 positive fermentation
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium genus ttest 3.2103 1.00e-10 positive nitrogen_fixation, aerobic_chemoheterotrophy
d__Bacteria;p__Deinococcota;c__Deinococci;o__Thermales;f__Thermaceae;g__Meiothermus genus ttest 3.1778 1.00e-10 positive
d__Bacteria;p__Armatimonadota phylum ttest 3.0966 1.00e-10 positive
d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;__;__;__ genus ttest 3.0814 1.00e-10 positive
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales order ttest 3.0073 1.33e-04 positive
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;__ family ttest 2.9326 1.00e-10 positive
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae family ttest 2.9083 2.13e-04 positive
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Features associated with nuclear_contamination_status=False

Feature Taxonomic Level Test Effect Size P-value Direction Functions
d__Bacteria;p__Actinobacteriota phylum ttest -43.7643 1.00e-10 negative
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria class ttest -30.2161 1.00e-10 negative
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales order ttest -26.1739 1.00e-10 negative
d__Bacteria;p__Acidobacteriota phylum ttest -24.8981 1.00e-10 negative
d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae class ttest -22.6807 1.00e-10 negative
d__Bacteria;p__Actinobacteriota;c__Actinobacteria class ttest -20.5215 4.80e-10 negative
d__Bacteria;p__Chloroflexi phylum ttest -19.2393 1.00e-10 negative
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae family ttest -16.6170 1.00e-10 negative dark_hydrogen_oxidation
d__Bacteria;p__Actinobacteriota;c__Thermoleophilia class ttest -14.3289 1.00e-10 negative
d__Bacteria;p__Planctomycetota phylum ttest -12.9499 5.67e-07 negative
d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria class ttest -12.0910 1.00e-10 negative
d__Bacteria;p__Verrucomicrobiota phylum ttest -11.9246 1.00e-10 negative
d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales order ttest -11.0172 1.00e-10 negative chemoheterotrophy
d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia class ttest -10.2659 1.00e-10 negative
d__Bacteria;p__Chloroflexi;c__Ktedonobacteria class ttest -10.2258 1.00e-10 negative
d__Bacteria;p__Planctomycetota;c__Planctomycetes class ttest -10.0868 5.87e-08 negative
d__Bacteria;p__Chloroflexi;c__Ktedonobacteria;o__Ktedonobacterales order ttest -9.5817 1.00e-10 negative
d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales order ttest -9.4309 1.00e-10 negative
d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales order ttest -8.5134 1.00e-10 negative
d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__Pedosphaeraceae family ttest -8.1764 1.00e-10 negative
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Features associated with facility_match=True

Feature Taxonomic Level Test Effect Size P-value Direction Functions
d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales order ttest 4.6825 6.76e-04 positive
d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae family ttest 4.0092 3.50e-03 positive
d__Bacteria;p__Chloroflexi;c__Anaerolineae class ttest 2.7563 2.10e-04 positive
d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae family ttest 1.7088 7.91e-04 positive
d__Bacteria;p__Planctomycetota;c__Planctomycetes;o__Pirellulales order ttest 1.6639 1.07e-02 positive
d__Bacteria;p__Planctomycetota;c__Planctomycetes;o__Pirellulales;f__Pirellulaceae family ttest 1.6362 1.25e-02 positive
d__Bacteria;p__Dependentiae;c__Babeliae class ttest 1.6175 3.97e-04 positive
d__Bacteria;p__Dependentiae phylum ttest 1.6163 4.26e-04 positive
d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales order ttest 1.5925 5.08e-04 positive
d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales order ttest 1.4246 4.90e-03 positive
d__Bacteria;p__Actinobacteriota;c__Actinobacteria;o__Micrococcales;f__Micrococcaceae;g__Arthrobacter genus ttest 1.1831 7.34e-08 positive
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales order ttest 1.1628 1.93e-02 positive
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae family ttest 1.1620 2.02e-02 positive
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae family ttest 1.1447 1.16e-02 positive
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;__ genus ttest 1.0911 1.12e-06 positive
d__Bacteria;p__Bacteroidota;c__Kryptonia;o__Kryptoniales order ttest 1.0469 6.09e-09 positive
d__Bacteria;p__Bacteroidota;c__Kryptonia class ttest 1.0131 1.30e-08 positive
d__Bacteria;p__Deinococcota;c__Deinococci;o__Thermales;f__Thermaceae;g__Meiothermus genus ttest 0.9870 1.24e-07 positive
d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Comamonadaceae;__ genus ttest 0.9743 9.01e-05 positive
d__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium genus ttest 0.9311 3.82e-09 positive
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Features associated with facility_match=False

Feature Taxonomic Level Test Effect Size P-value Direction Functions
d__Bacteria;p__Actinobacteriota phylum ttest -20.5596 5.06e-07 negative
d__Bacteria;p__Actinobacteriota;c__Actinobacteria class ttest -9.1096 5.66e-04 negative
d__Bacteria;p__Chloroflexi phylum ttest -9.0144 1.35e-08 negative
d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae class ttest -8.9620 1.00e-10 negative
d__Bacteria;p__Acidobacteriota phylum ttest -8.6943 1.62e-05 negative
d__Bacteria;p__Acidobacteriota;c__Acidobacteriae class ttest -8.2788 1.00e-10 negative
d__Bacteria;p__Chloroflexi;c__Ktedonobacteria class ttest -8.0614 1.00e-10 negative
d__Bacteria;p__Chloroflexi;c__Ktedonobacteria;o__Ktedonobacterales order ttest -7.9343 1.00e-10 negative
d__Bacteria;p__Actinobacteriota;c__Thermoleophilia class ttest -7.0425 2.15e-09 negative
d__Bacteria;p__Chloroflexi;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae family ttest -6.5576 1.00e-10 negative
d__Bacteria;p__Patescibacteria phylum ttest -6.3152 6.56e-08 negative
d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales order ttest -5.6075 1.00e-10 negative
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae family ttest -5.2622 1.00e-10 negative dark_hydrogen_oxidation
d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia class ttest -4.9436 1.70e-09 negative
d__Bacteria;p__Verrucomicrobiota phylum ttest -4.6567 3.80e-06 negative
d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales order ttest -4.4163 1.00e-10 negative
d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales order ttest -3.9320 1.00e-10 negative
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales order ttest -3.9287 2.10e-02 negative
d__Bacteria;p__Patescibacteria;c__Saccharimonadia class ttest -3.8442 1.00e-10 negative
d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales order ttest -3.5051 2.13e-10 negative
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Statistical Summary

Column Table Type Test Level Significant Features Total Features
nuclear_contamination_status raw mwu_bonferroni phylum 41 41
nuclear_contamination_status raw kruskal_bonferroni phylum 41 41
nuclear_contamination_status raw mwu_bonferroni class 125 125
nuclear_contamination_status raw kruskal_bonferroni class 125 125
nuclear_contamination_status raw mwu_bonferroni order 243 243
nuclear_contamination_status raw kruskal_bonferroni order 243 243
nuclear_contamination_status raw mwu_bonferroni family 405 405
nuclear_contamination_status raw kruskal_bonferroni family 405 405
nuclear_contamination_status raw mwu_bonferroni genus 644 644
nuclear_contamination_status raw kruskal_bonferroni genus 644 644
nuclear_contamination_status filtered mwu_bonferroni phylum 41 41
nuclear_contamination_status filtered kruskal_bonferroni phylum 41 41
nuclear_contamination_status filtered mwu_bonferroni class 125 125
nuclear_contamination_status filtered kruskal_bonferroni class 125 125
nuclear_contamination_status filtered mwu_bonferroni order 243 243
nuclear_contamination_status filtered kruskal_bonferroni order 243 243
nuclear_contamination_status filtered mwu_bonferroni family 405 405
nuclear_contamination_status filtered kruskal_bonferroni family 405 405
nuclear_contamination_status filtered mwu_bonferroni genus 644 644
nuclear_contamination_status filtered kruskal_bonferroni genus 644 644
nuclear_contamination_status normalized ttest phylum 81 81
nuclear_contamination_status normalized mwu_bonferroni phylum 41 41
nuclear_contamination_status normalized kruskal_bonferroni phylum 41 41
nuclear_contamination_status normalized ttest class 227 227
nuclear_contamination_status normalized mwu_bonferroni class 125 125
nuclear_contamination_status normalized kruskal_bonferroni class 125 125
nuclear_contamination_status normalized ttest order 573 573
nuclear_contamination_status normalized mwu_bonferroni order 243 243
nuclear_contamination_status normalized kruskal_bonferroni order 243 243
nuclear_contamination_status normalized ttest family 973 973
nuclear_contamination_status normalized mwu_bonferroni family 405 405
nuclear_contamination_status normalized kruskal_bonferroni family 405 405
nuclear_contamination_status normalized ttest genus 2126 2126
nuclear_contamination_status normalized mwu_bonferroni genus 644 644
nuclear_contamination_status normalized kruskal_bonferroni genus 644 644
nuclear_contamination_status clr_transformed ttest phylum 22 22
nuclear_contamination_status clr_transformed mwu_bonferroni phylum 13 13
nuclear_contamination_status clr_transformed kruskal_bonferroni phylum 13 13
nuclear_contamination_status clr_transformed ttest class 68 68
nuclear_contamination_status clr_transformed mwu_bonferroni class 43 43
nuclear_contamination_status clr_transformed kruskal_bonferroni class 43 43
nuclear_contamination_status clr_transformed ttest order 149 149
nuclear_contamination_status clr_transformed mwu_bonferroni order 85 85
nuclear_contamination_status clr_transformed kruskal_bonferroni order 85 85
nuclear_contamination_status clr_transformed ttest family 229 229
nuclear_contamination_status clr_transformed mwu_bonferroni family 123 123
nuclear_contamination_status clr_transformed kruskal_bonferroni family 123 123
nuclear_contamination_status clr_transformed ttest genus 396 396
nuclear_contamination_status clr_transformed mwu_bonferroni genus 196 196
nuclear_contamination_status clr_transformed kruskal_bonferroni genus 196 196
nuclear_contamination_status presence_absence fisher phylum 21 21
nuclear_contamination_status presence_absence fisher class 55 55
nuclear_contamination_status presence_absence fisher order 129 129
nuclear_contamination_status presence_absence fisher family 223 223
nuclear_contamination_status presence_absence fisher genus 375 375
facility_match raw mwu_bonferroni phylum 59 59
facility_match raw kruskal_bonferroni phylum 59 59
facility_match raw mwu_bonferroni class 137 137
facility_match raw kruskal_bonferroni class 137 137
facility_match raw mwu_bonferroni order 270 270
facility_match raw kruskal_bonferroni order 270 270
facility_match raw mwu_bonferroni family 416 416
facility_match raw kruskal_bonferroni family 416 416
facility_match raw mwu_bonferroni genus 712 712
facility_match raw kruskal_bonferroni genus 712 712
facility_match filtered mwu_bonferroni phylum 59 59
facility_match filtered kruskal_bonferroni phylum 59 59
facility_match filtered mwu_bonferroni class 137 137
facility_match filtered kruskal_bonferroni class 137 137
facility_match filtered mwu_bonferroni order 270 270
facility_match filtered kruskal_bonferroni order 270 270
facility_match filtered mwu_bonferroni family 416 416
facility_match filtered kruskal_bonferroni family 416 416
facility_match filtered mwu_bonferroni genus 712 712
facility_match filtered kruskal_bonferroni genus 712 712
facility_match normalized ttest phylum 71 71
facility_match normalized mwu_bonferroni phylum 59 59
facility_match normalized kruskal_bonferroni phylum 59 59
facility_match normalized ttest class 182 182
facility_match normalized mwu_bonferroni class 137 137
facility_match normalized kruskal_bonferroni class 137 137
facility_match normalized ttest order 402 402
facility_match normalized mwu_bonferroni order 270 270
facility_match normalized kruskal_bonferroni order 270 270
facility_match normalized ttest family 662 662
facility_match normalized mwu_bonferroni family 416 416
facility_match normalized kruskal_bonferroni family 416 416
facility_match normalized ttest genus 1340 1340
facility_match normalized mwu_bonferroni genus 712 712
facility_match normalized kruskal_bonferroni genus 712 712
facility_match clr_transformed ttest phylum 16 16
facility_match clr_transformed mwu_bonferroni phylum 9 9
facility_match clr_transformed kruskal_bonferroni phylum 9 9
facility_match clr_transformed ttest class 50 50
facility_match clr_transformed mwu_bonferroni class 20 20
facility_match clr_transformed kruskal_bonferroni class 20 20
facility_match clr_transformed ttest order 114 114
facility_match clr_transformed mwu_bonferroni order 42 42
facility_match clr_transformed kruskal_bonferroni order 42 42
facility_match clr_transformed ttest family 180 180
facility_match clr_transformed mwu_bonferroni family 59 59
facility_match clr_transformed kruskal_bonferroni family 59 59
facility_match clr_transformed ttest genus 288 288
facility_match clr_transformed mwu_bonferroni genus 48 48
facility_match clr_transformed kruskal_bonferroni genus 48 48
facility_match presence_absence fisher phylum 18 18
facility_match presence_absence fisher class 44 44
facility_match presence_absence fisher order 93 93
facility_match presence_absence fisher family 144 144
facility_match presence_absence fisher genus 279 279
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Machine Learning Results

Model Performance

Table Type Level Method Top Features Accuracy F1 ScoreBalance between precision and recall... MCCBalanced classifier metric (-1 to 1) that considers all confusion matrix values... ROC AUCProbability that random positive ranks higher than random negative... PR AUCPositive-class focused metric for imbalanced data...
normalized phylum rfe 29 0.9966 0.9344 0.9339 0.9990 0.9677
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Top Features by Importance

Table Type Level Method Rank Feature Importance
normalized phylum rfe 1 d__Bacteria;p__Verrucomicrobiota 19.1296
normalized phylum rfe 2 d__Bacteria;p__Bacteroidota 16.9407
normalized phylum rfe 3 d__Bacteria;p__Proteobacteria 12.5686
normalized phylum rfe 4 d__Bacteria;p__Planctomycetota 7.2250
normalized phylum rfe 5 d__Bacteria;__ 7.1208
normalized phylum rfe 6 d__Bacteria;p__Actinobacteriota 6.6038
normalized phylum rfe 7 d__Bacteria;p__Bdellovibrionota 4.2065
normalized phylum rfe 8 d__Bacteria;p__Patescibacteria 3.4625
normalized phylum rfe 9 d__Bacteria;p__Myxococcota 3.3626
normalized phylum rfe 10 d__Bacteria;p__Elusimicrobiota 3.0188
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SHAP Analysis

Comprehensive SHAP analysis for top features across all models:

Table Type Level Method Feature Mean |SHAP| Beeswarm Interpretation Spearman's ρ Dependency plot interpretation Relationship Partner Feature Interaction Strength Relationship ρ (Feature) ρ (Partner)
normalized phylum rfe d__Bacteria;p__Verrucomicrobiota higher → lower prediction -0.80 d__Bacteria;p__Actinobacteriota 0.156 mutually diminishing -0.57 -0.41
normalized phylum rfe d__Bacteria;p__Bacteroidota higher → higher prediction 0.97 d__Bacteria;p__Actinobacteriota 0.118 opposing or balancing -0.30 0.33
normalized phylum rfe d__Bacteria;p__Actinobacteriota higher → lower prediction -0.85 d__Bacteria;p__Verrucomicrobiota 0.156 mutually diminishing -0.41 -0.57
normalized phylum rfe d__Bacteria;p__Proteobacteria higher → higher prediction 0.36 d__Bacteria;p__Actinobacteriota 0.127 opposing or balancing -0.31 0.47
normalized phylum rfe d__Bacteria;p__Elusimicrobiota higher → higher prediction 0.71 d__Bacteria;p__Armatimonadota 0.029 mutually reinforcing 0.21 0.07
normalized phylum rfe d__Bacteria;__ higher → higher prediction 0.53 d__Bacteria;p__Proteobacteria 0.059 opposing or balancing -0.04 0.01
normalized phylum rfe d__Bacteria;p__Bdellovibrionota higher → higher prediction 0.78 d__Bacteria;__ 0.049 mutually reinforcing 0.07 0.27
normalized phylum rfe d__Bacteria;p__Planctomycetota higher → higher prediction 0.18 d__Bacteria;p__Verrucomicrobiota 0.120 mutually diminishing -0.82 -0.12
normalized phylum rfe d__Bacteria;p__Myxococcota higher → higher prediction 0.74 d__Bacteria;p__Proteobacteria 0.081 mutually reinforcing 0.30 0.51
normalized phylum rfe d__Bacteria;p__Armatimonadota higher → higher prediction 0.82 d__Bacteria;p__Elusimicrobiota 0.029 mutually reinforcing 0.07 0.21
normalized phylum rfe d__Bacteria;p__Cyanobacteria higher → higher prediction 0.43 d__Bacteria;p__Bacteroidota 0.030 mutually reinforcing 0.45 0.01
normalized phylum rfe d__Bacteria;p__Patescibacteria higher → lower prediction -0.69 d__Bacteria;p__Proteobacteria 0.095 opposing or balancing 0.30 -0.15
normalized phylum rfe Unassigned;__ higher → lower prediction -0.75 d__Bacteria;p__Actinobacteriota 0.071 mutually reinforcing 0.55 0.30
normalized phylum rfe d__Bacteria;p__Cloacimonadota higher → higher prediction 0.26 d__Bacteria;p__Verrucomicrobiota 0.019 opposing or balancing 0.04 -0.70
normalized phylum rfe d__Bacteria;p__Latescibacterota higher → lower prediction -0.51 d__Bacteria;__ 0.016 mutually reinforcing 0.13 0.09
normalized phylum rfe d__Bacteria;p__Chloroflexi higher → lower prediction -0.78 d__Bacteria;p__Planctomycetota 0.025 mutually diminishing -0.21 -0.53
normalized phylum rfe d__Bacteria;p__FCPU426 higher → higher prediction 0.35 d__Bacteria;p__Verrucomicrobiota 0.004 opposing or balancing -0.04 0.57
normalized phylum rfe d__Archaea;p__Crenarchaeota higher → lower prediction -0.05 d__Bacteria;p__Planctomycetota 0.026 mutually diminishing -0.13 -0.49
normalized phylum rfe d__Bacteria;p__Deinococcota higher → lower prediction -0.27 d__Bacteria;__ 0.020 opposing or balancing 0.05 -0.26
normalized phylum rfe d__Archaea;p__Thermoplasmatota higher → lower prediction -0.32 d__Bacteria;p__Bacteroidota 0.008 mutually reinforcing 0.19 0.05
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Alpha_Diversity

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Shap

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Violin

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